Oncogenic structural variants

Abstract

The technology relates in part to methods and compositions for detecting oncogenic structural variants.

What is claimed is: 
     
         1 . A method for detecting the presence or absence of a structural variant in a sample, the method comprising:
 a) performing a nucleic acid analysis on a sample obtained from a subject; and   b) detecting whether a structural variant is present or absent in the sample according to the analysis in (a), wherein a breakpoint of the structural variant maps to a location between positions selected from the group consisting of: positions listed in row 5, row 6, row 22, and row 23 of Table 10, wherein the positions are in an HG38 human reference genome.   
     
     
         2 . The method of  claim 1 , wherein the ectopic portion is located at a position in spatial proximity to a cancer gene selected from the group consisting of: cancer genes in row 7 and row 15 of Table 10. 
     
     
         3 . The method of  claim 1 , wherein the ectopic portion is located at a position in linear proximity to a cancer gene selected from the group consisting of: cancer genes in row 7 and row 15 of Table 10. 
     
     
         4 . The method of  claim 1 , wherein the structural variant comprises an ectopic portion of genomic DNA from a chromosome, wherein, in an HG38 human reference genome, the ectopic portion of genomic DNA maps to a region of a chromosome outside of positions selected from the group consisting of: positions listed in row 5 and row 6 of Table 10. 
     
     
         5 . The method of  claim 1 , wherein the structural variant comprises an ectopic portion of genomic DNA maps to a region of a chromosome outside of positions selected from the group consisting of: positions listed in row 22 and row 23 of Table 10. 
     
     
         6 . The method of  claim 1 , wherein the nucleic acid analysis in (a) comprises a method that preserves spatial-proximal contiguity information. 
     
     
         7 . The method of  claim 1 , wherein the nucleic acid analysis in (a) comprises generating proximity ligated nucleic acid molecules. 
     
     
         8 . A method for detecting the presence or absence of a structural variant in a sample, the method comprising:
 a) performing a nucleic acid analysis on a sample obtained from a subject; and   b) detecting whether a structural variant is present or absent in the sample according to the analysis in (a), wherein the structural variant comprises an ectopic portion of genomic DNA from positions selected from the group consisting of: positions listed in row 5, row 6, row 22, and row 23 of Table 10, wherein the ectopic portion is located at a position in proximity to a cancer gene selected from the group consisting of: cancer genes in row 7 and row 15 of Table 10.   
     
     
         9 . The method of  claim 8 , wherein the ectopic portion is located at a position in spatial proximity to a cancer gene selected from the group consisting of: cancer genes in row 7 and row 15 of Table 10. 
     
     
         10 . The method of  claim 8 , wherein the ectopic portion is located at a position in linear proximity to a cancer gene selected from the group consisting of: cancer genes in row 7 and row 15 of Table 10. 
     
     
         11 . The method of  claim 8 , wherein the structural variant comprises an ectopic portion of genomic DNA from a chromosome, wherein, in an HG38 human reference genome, the ectopic portion of genomic DNA maps to a region of a chromosome outside of positions selected from the group consisting of: positions listed in row 5 and row 6 of Table 10. 
     
     
         12 . The method of  claim 8 , wherein the structural variant comprises an ectopic portion of genomic DNA maps to a region of a chromosome outside of positions selected from the group consisting of: positions listed in row 22 and row 23 of Table 10. 
     
     
         13 . The method of  claim 8 , wherein the nucleic acid analysis in (a) comprises a method that preserves spatial-proximal contiguity information. 
     
     
         14 . The method of  claim 8 , wherein the nucleic acid analysis in (a) comprises generating proximity ligated nucleic acid molecules. 
     
     
         15 . A composition, comprising:
 a synthetic oligonucleotide 10 to 500 consecutive nucleotides in length comprising:   (i) a first polynucleotide identical to or complementary to a subsequence of 5 or more consecutive nucleotides in length within a region of a chromosome, wherein the region spans positions selected from the groups consisting of: positions listed in row 5 and row 6 of Table 10; and   (ii) a second polynucleotide identical to or complementary to a subsequence of about 5 or more consecutive nucleotides in length within a region of a chromosome, wherein the region spans positions selected from the groups consisting of: positions listed in row 22 and row 23 of Table 10; and wherein:
 the positions are in the HG38 human reference genome, and 
 the synthetic oligonucleotide specifically hybridizes under stringent hybridization conditions to a target sequence comprising the subsequence of (i) and the subsequence of (ii). 
   
     
     
         16 . A composition, comprising:
 (a) a first synthetic oligonucleotide 10 to 500 consecutive nucleotides in length comprising a first polynucleotide identical to or complementary to a subsequence of 5 or more consecutive nucleotides in length within a region of a chromosome, wherein the region spans positions selected from the groups consisting of: positions listed in row 5 and row 6 of Table 10; and   (b) a second synthetic oligonucleotide 10 to 500 consecutive nucleotides in length comprising a second polynucleotide identical to or complementary to a subsequence of about 5 or more consecutive nucleotides in length within a region of a chromosome, wherein the region spans positions selected from the groups consisting of: positions listed in row 22 and row 23 of Table 10; wherein:   the positions are in the HG38 human reference genome,   the first synthetic oligonucleotide specifically hybridizes under stringent hybridization conditions to a target nucleic acid comprising the subsequence in (a), and   the second synthetic oligonucleotide specifically hybridizes under stringent hybridization conditions to a target nucleic acid comprising the subsequence in (b).   
     
     
         17 . The composition of  claim 16 , wherein:
 the first synthetic oligonucleotide specifically hybridizes under stringent hybridization conditions to a target nucleic acid comprising the subsequence of (a) and does not specifically hybridize to a target nucleic acid comprising the subsequence of (b), and   the second synthetic oligonucleotide specifically hybridizes under stringent hybridization conditions to a target nucleic acid comprising the subsequence of (b) and does not specifically hybridize to a target nucleic acid comprising the subsequence of (a).   
     
     
         18 . A composition comprising synthetic oligonucleotides selected from the group consisting of: the synthetic oligonucleotides of  claim 15, claim 16, and 17 . 
     
     
         19 . A kit comprising synthetic oligonucleotides selected from the group consisting of: the synthetic oligonucleotides of  claim 15, claim 16, and 17 .